Bio/PopGen/IndividualI.pm

   1 # $Id $
   2 #
   3 # BioPerl module for Bio::PopGen::IndividualI
   4 #
   5 # Cared for by Jason Stajich <jason-at-bioperl.org>
   6 #
   7 # Copyright Jason Stajich
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::PopGen::IndividualI - An individual who has Genotype or Sequence Results
  16
  17 =head1 SYNOPSIS
  18
  19   # Get a Bio::PopGen::IndividualI somehow
  20   # test if it has alleles/genotypes for a given marker
  21   if( $ind->has_marker($markername) ) {
  22   }
  23   # get the unique id
  24   print $ind->unique_id, "\n";
  25
  26   # get the number of results (genotypes)
  27   print $ind->num_results;
  28
  29 =head1 DESCRIPTION
  30
  31 Describe the interface here
  32
  33 =head1 FEEDBACK
  34
  35 =head2 Mailing Lists
  36
  37 User feedback is an integral part of the evolution of this and other
  38 Bioperl modules. Send your comments and suggestions preferably to
  39 the Bioperl mailing list.  Your participation is much appreciated.
  40
  41   bioperl-l@bioperl.org                  - General discussion
  42   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  43
  44 =head2 Reporting Bugs
  45
  46 Report bugs to the Bioperl bug tracking system to help us keep track
  47 of the bugs and their resolution. Bug reports can be submitted via
  48 email or the web:
  49
  50   http://bugzilla.open-bio.org/
  51
  52 =head1 AUTHOR - Jason Stajich
  53
  54 Email jason-at-bioperl.org
  55
  56 =head1 APPENDIX
  57
  58 The rest of the documentation details each of the object methods.
  59 Internal methods are usually preceded with a _
  60
  61 =cut
  62
  63
  64 # Let the code begin...
  65
  66
  67 package Bio::PopGen::IndividualI;
  68 use strict;
  69
  70
  71 use base qw(Bio::Root::RootI);
  72
  73
  74 =head2 unique_id
  75
  76  Title   : unique_id
  77  Usage   : my $id = $individual->unique_id
  78  Function: Unique Identifier
  79  Returns : string representing unique identifier
  80  Args    : string
  81
  82
  83 =cut
  84
  85 sub unique_id{
  86    my ($self) = @_;
  87    $self->throw_not_implemented();
  88 }
  89
  90
  91 =head2 num_genotypes
  92
  93  Title   : num_genotypes
  94  Usage   : my $count = $person->num_results;
  95  Function: returns the count of the number of Results for a person
  96  Returns : integer
  97  Args    : none
  98
  99 =cut
 100
 101 sub num_genotypes {
 102     shift->throw_not_implemented;
 103 }
 104
 105 sub num_of_results{
 106     my $self = shift;
 107     $self->deprecated("num_of_results is deprecated, use num_genotypes instead");
 108     $self->num_genotypes;
 109 }
 110
 111 =head2 get_Genotypes
 112
 113  Title   : get_Genotypes
 114  Usage   : my @genotypes = $ind->get_Genotypes(-marker => $markername);
 115  Function: Get the genotypes for an individual, based on a criteria
 116  Returns : Array of genotypes
 117  Args    : either none (return all genotypes) or
 118            -marker => name of marker to return (exact match, case matters)
 119
 120
 121 =cut
 122
 123 sub get_Genotypes{
 124     my ($self) = @_;
 125     $self->throw_not_implemented();
 126 }
 127
 128 =head2 has_Marker
 129
 130  Title   : has_Marker
 131  Usage   : if( $ind->has_Marker($name) ) {}
 132  Function: Boolean test to see if an Individual has a genotype
 133            for a specific marker
 134  Returns : Boolean (true or false)
 135  Args    : String representing a marker name
 136
 137
 138 =cut
 139
 140 sub has_Marker{
 141    my ($self,$name) = @_;
 142    $self->throw_not_implemented();
 143 }
 144
 145 =head2 get_marker_names
 146
 147  Title   : get_marker_names
 148  Usage   : my @names = $individual->get_marker_names;
 149  Function: Returns the list of known marker names
 150  Returns : List of strings
 151  Args    : none
 152
 153
 154 =cut
 155
 156 sub get_marker_names{
 157    my ($self) = @_;
 158    $self->throw_not_implemented();
 159 }
 160
 161
 162 1;